Thank you Christoph for your help. I figured the issue out using csg_map. Thank you again for your guidance and support.
Thank you Kind Regards, Akash On Tue, May 19, 2020 at 2:06 PM Christoph Junghans <[email protected]> wrote: > On Tue, May 19, 2020 at 11:58 AM Akash Banerjee <[email protected]> > wrote: > > > > Hi Votca Development team, > > > > I am trying to validate the coarse grained bond distributions against > the all-atom bond distributions. In my case, the bond.dist.tgt file ( > dumped by using csg_stat on all atom files) gives different results as > compared to using my own analysis tool. > > I am assuming the bond.dist.tgt files have been generated using a Center > of Mass framework for all coarse grained fragments. > For VOTCA the mapping is whatever you put in the mapping file, it > isn't COM by default. > > > Also, I used the GROMACS analysis tool to find the bonded distribution > in the all-atom model. The result turned out to be very different from > bond.dist.tgt. > > > > Please help me understand how bond.dist.tgt is derived. This information > would help me validate distributions between AA and CG scales. > The first step would be to check if your mapping is right, you could > run csg_map on the initial condition (conf.gro) and then overlay the > output in VMD to see if the cg beads are in the right spots. > > Christoph > > > > Thank you for your help in advance. > > > > Kind Regards, > > Akash > > > > -- > > Join us on Slack: https://join.slack.com/t/votca/signup > > --- > > You received this message because you are subscribed to the Google > Groups "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/6c2ac9ed-5acb-4f3e-a267-9a1a43884224%40googlegroups.com > . > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e4YxrJXOtT-GhMKwQm2-ANuf%2BTQ2SEbQmyfT%3DNv%2B5iSLQ%40mail.gmail.com > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CABWEH%3DoCPLCFPkyxQTUP-ax0oO3o%3DGwmQ_D_Mf1j388HwrXeyw%40mail.gmail.com.
